Awhile after it was revealed that Stefan was Nikolas' father, it was revealed that Helena set the whole thing up to make Stefan think that he was Nikolas' father so that he would treat Nikoas as a son or mess with his mind or some such Helena like plot. Stavros was really Nikolas' father the whole time.
Lissie's Fics:
http://www.network54.com/Forum/181424